Quality report of the IPBES IAS bibliography

Bibplography

Bibliography Setup

The bibliography is loaded and the DOIs, ISBNs and ISSNs are extracted.

Introduction

This report assesses the following in regards to the provided bibliography named bibliography:

Remarks: - Group ID is in the json, but not in the csv. The group ID makes it possible to directly jump to the reference in the Zotero Library online.

Data Quality of the Bibliography

Cleanliness of bibliography

One measure of the cleanliness of a Bibliography is assessed by checking the number of references that have a DOI. The following table gives an overview over some numbers regarding the DOIs, ISBNs and ISSNs in the bibliography.

Entries with DOIs, ISBNs or ISSNs

To identify a reference, the most widely used identifier is the DOI. The following table shows the number of references with a DOI and the number of unique DOIs.

To consider duplicate ISBNs or ISSNs as duplicates entries in the library is not waranted as e.g. differenc chapters of a book can be separate entries in the library and therefore lead toi duplicates.

  • DOIs: 996 (80.0643087%) - 70 duplicates
  • ISBNss: 16 (1.2861736%) - 443 duplicates
  • ISBNss: 953 (76.607717%) - 593 duplicates

The following DOIs are duplicates in the bibliography. This table should be empty.

Show the code
#|
if (sum(duplicated(bibliography$dois)) > 0) {
    data <- data.frame(
        Type = "doi",
        Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', bibliography$dois[duplicated(bibliography$dois)], bibliography$dois[duplicated(bibliography$dois)])
    )
} else {
    data <- data.frame(
        Type = "doi",
        Identifier = NA
    )
}

data |>
    knitr::kable(
        caption = "Duplicate DOIs in the Bibliography",
        escape = FALSE
    )
Duplicate DOIs in the Bibliography
Type Identifier
doi 10.1111/1365-2664.12385
doi 10.1111/j.1461-0248.2007.01061.x
doi 10.1098/rspb.2004.2909
doi 10.3896/ibra.1.50.1.02
doi 10.1111/j.1365-2745.2012.01968.x
doi 10.1890/120321
doi 10.1890/03-5271
doi 10.1016/j.biocon.2012.10.021
doi 10.1111/j.1600-0706.2013.00644.x
doi 10.1046/j.1472-4642.2002.00148.x
doi 10.1126/science.1257259
doi 10.1111/j.1442-9993.2004.01376.x
doi 10.1371/journal.pone.0002771
doi 10.1007/s13592-014-0316-z
doi 10.1111/j.1365-2311.2010.01234.x
doi 10.1007/s10144-006-0010-8
doi 10.1146/annurev.ecolsys.34.011802.132355
doi 10.1073/pnas.1115559108
doi 10.1073/pnas.1218503110
doi 10.1126/science.1127863
doi 10.1016/j.baae.2010.01.001
doi 10.1073/pnas.1323073111
doi 10.1016/j.biocon.2005.11.013
doi 10.3896/ibra.1.52.4.12
doi 10.1371/journal.pone.0030641
doi 10.1016/j.cub.2008.08.066
doi 10.1073/pnas.1218503110
doi 10.1146/annurev.ecolsys.38.091206.095818
doi 10.1073/pnas.1307438110
doi 10.1079/ijt20048
doi 10.1111/j.1461-0248.2010.01579.x
doi 10.1098/rspb.2014.1799
doi 10.1111/ele.12325
doi 10.1051/apido:2006027
doi 10.1371/journal.pone.0021363
doi 10.1038/nature10452
doi 10.1016/j.ecolecon.2008.06.014
doi 10.1073/pnas.1012431108
doi 10.1890/130330
doi 10.1126/science.1230200
doi 10.1111/j.1461-0248.2011.01669.x
doi 10.26786/1920-7603(2014)1
doi 10.1126/science.1185383
doi 10.1016/j.tree.2013.05.008
doi 10.1098/rspb.2014.1358
doi 10.1016/j.ppees.2010.02.005
doi 10.1146/annurev.en.28.010183.002203
doi 10.1098/rspb.2006.3721
doi 10.1073/pnas.262413599
doi 10.1111/j.1461-0248.2007.01018.x
doi 10.4039/ent133439-4
doi 10.1371/journal.pone.0035954
doi 10.1098/rspb.2004.2909
doi 10.2980/i1195-6860-12-3-289.1
doi 10.1111/j.1600-0706.2010.18644.x
doi 10.1111/j.1461-0248.2008.01170.x
doi 10.1016/j.tree.2010.01.007
doi 10.1080/0005772x.2001.11099523
doi 10.2307/3071954
doi 10.1111/j.1469-185x.2011.00216.x
doi 10.1146/annurev-ecolsys-102710-145042
doi 10.1111/j.1461-0248.2008.01269.x
doi 10.1098/rspb.2008.0405
doi 10.1111/j.1523-1739.2009.01331.x
doi 10.1146/annurev.en.22.010177.001141
doi 10.1146/annurev.ecolsys.29.1.83
doi 10.1126/science.aaa7031
doi 10.1016/j.biocon.2006.07.023
doi 10.1017/s0889189300003179
doi 10.1111/ele.12121
Show the code
rm(data)

DOIs in Open Alex

To validate the existence and validity of the DOIs, we check if the DOIs are in the OpenAlex database.

Of the 926 unique DOIs in the library, 50 (5.399568%) are in not in OpenAlex.

Show the code
data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa, metrics$dois_not_in_oa)
) |>
    IPBES.R::table_dt(caption = "dois_not_in_oa")

Of these -863 are not valid. These are:

Show the code
data.frame(
    Type = "doi",
    Identifier = sprintf('<a href="https://doi.org/%s" target="_blank">%s</a>', metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)], metrics$dois_not_in_oa[!(metrics$dois_not_in_oa %in% metrics$dois_valid)])
) |>
    knitr::kable(
        caption = "Non Valid DOIs in the Bibliography",
        escape = FALSE
    )

TODO Finally we check, if these dois exist but are not ingested into OpanAlex. This is done using the doi.org resolver This is disabled at the moment.

Show the code
to_check <- bibliography$dois[!(bibliography$dois %in% dois_works)]

dois_valid <- IPBES.R::doi_valid(bibliography$dois)
dois_openalex <- bibliography$dois %in% dois_works
names(dois_openalex) <- bibliography$dois

dois_exist <- IPBES.R::doi_exists(to_check, cache_file = file.path(".", "cache", "doi_exist.rds"))
dois_not_retracted <- IPBES.R::doi_not_retracted(bibliography$dois, cache_file = file.path(".", "cache", "doi_not_retracted.rds"))

sprintf(
    fmt = paste(
        "Number of references: \t\t %d",
        "Number of DOIs: \t\t %d",
        "Number of Duplicate DOIs: \t %d",
        "Number of DOIs in OpenAlex: \t %d ( %f %)",
        "Number of Existing DOIs: \t %d",
        "Number of Retracted DOIs: \t %d",
        "Percentage of Duplicate DOIs: \t %f",
        sep = "\n"
    ),
    nrow(bibliography),
    sum(!is.na(bibliography$dois)),
    length(bibliography$dois) - length(unique((bibliography$dois))),
    sum(dois_openalex), 100 * sum(dois_openalex) / nrow(bibliography),
    sum(dois_exist),
    sum(!dois_not_retracted),
    ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100
) |> cat()
Show the code
oldopts <- options(knitr.kable.NA = "")
data.frame(
    metrics = c(
        "# References",
        "**DOI**",
        "# DOIs",
        "# Duplicate DOIs",
        "# Existing DOIs",
        "# Retracted DOIs",
        "% Duplicate DOIs",
        "**ISBN**",
        "# ISBNs",
        "# Duplicate ISBNs",
        "**ISSN**",
        "# ISSNs",
        "# Duplicate ISSNs"
    ),
    Value = c(
        nrow(bibliography),
        NA,
        sum(!is.na(bibliography$dois)),
        length(bibliography$dois) - length(unique((bibliography$dois))),
        sum(dois_exist),
        sum(!dois_not_retracted),
        ((dois_valid |> unique() |> length()) / length(dois_valid)) |> round(digits = 3) * 100,
        NA,
        sum(!is.na(bibliography$isbns)),
        length(bibliography$isbns) - length(unique((bibliography$isbns))),
        NA,
        sum(!is.na(bibliography$issns)),
        length(bibliography$issns) - length(unique((bibliography$issns)))
    )
) |>
    knitr::kable(
        caption = "Cleanliness of the Bibliography",
    )
options(oldopts)

Contentual and Bibliographic analysis

Publication types

Show the code
bibliography$bibliography |>
    dplyr::group_by(
        Item.Type
    ) |>
    dplyr::summarize(
        count = n()
    ) |>
    dplyr::arrange(
        desc(count)
    ) |>
    knitr::kable()
Item.Type count
journalArticle 1148
book 39
manuscript 20
bookSection 15
conferencePaper 9
report 4
thesis 3
artwork 2
document 2
webpage 2

Year of Publication

Show the code
params$figure_pub_year
NULL

Access Status of References

This is checked by using the OpenAlex retrieved works. Therefore it is li=mited to the works that are on OpenAlex. At the moment, only references with a DOI were retrieved from OpenAlex.

Show the code
params$figure_oa_status
NULL

50 Most often cited Journals

Show the code
params$figure_top_journals
NULL

This table contains all Journals as specified in the Zotero database.

Show the code
params$figure_top_journals_data |>
    IPBES.R::table_dt("cited_journals")

TODO Coutries of Institutes of all authors

This plot only contains the countries with more than 10 references.

Show the code
#|
#| fig-height: 10
#| fig-width: 10

params$figure_top_countries

This table contains all countries and the number of authorship.

Show the code
params$figure_top_country_data |>
    IPBES.R::table_dt("top_countries")